"Chobani markets its Greek yogurt as containing only natural ingredients, but it has received complaints from consumer advocacy groups for its use of milk that comes from dairy cows fed with GMO animal feed," WSJ writes.

The Greek yogurt manufacturer's business has exploded in recent years on increased demand for the thick and creamy yogurt.

But the Whole Foods' snub is Chobani's second disaster this year.

In September, Chobani recalled 35 flavors of yogurt after more than 100 people reportedly fell ill after eating it.